x2p {mmtsne}

Data to probability matrix

Description

x2p returns a pair-wise conditional probability matrix given an input matrix X.

Usage

x2p(X, perplexity = 30, tol = 1e-05)

Arguments

X

A data matrix with N rows.

perplexity

The target perplexity. Values between 5 and 50 are generally considered appropriate. Loosely translates into the expected number of neighbors per point.

tol

A small positive value.

Details

This function is an almost direct port of the original Python implementation by van der Maaten and Hinton (2008). It uses a binary search to estimate probability values for all pairwise-elements of X. The conditional Gaussian distributions should all be of equal perplexity.

Value

An N x N matrix of pair-wise probabilities.

References

L.J.P. van der Maaten and G.E. Hinton. “Visualizing High-Dimensional Data Using t-SNE.” Journal of Machine Learning Research 9(Nov):2579-2605, 2008. PDF.